Search

Sequential, multiple assignment, randomized trial (SMART) designs are appropriate for comparing adaptive treatment interventions, in which intermediate outcomes (called tailoring variables) guide subsequent treatment decisions for individual patients. Within a SMART design, patients may be re-randomized to subsequent treatments following the outcomes of their intermediate assessments. In this paper, we provide an overview of statistical considerations necessary to design and implement a two-stage SMART design with a binary tailoring variable and a survival final endpoint. A chronic lymphocytic leukemia trial with a final endpoint of progression-free survival is used as an example for the simulations to assess how design parameters, including, choice of randomization ratios for each stage of randomization, and response rates of the tailoring variable affect the statistical power. We assess the choice of weights from restricted re-randomization on data analyses and appropriate hazard rate assumptions. Specifically, for a given first-stage therapy and prior to the tailoring variable assessment, we assume equal hazard rates for all patients randomized to a treatment arm. After the tailoring variable assessment, individual hazard rates are assumed for each intervention path. Simulation studies demonstrate that the response rate of the binary tailoring variable impacts power as it directly impacts the distribution of patients. We also confirm that when the first stage randomization is 1:1, it is not necessary to consider the first stage randomization ratio when applying the weights. We provide an R-shiny application for obtaining power for a given sample size for SMART designs. [ABSTRACT FROM AUTHOR]

Background/aim: Single-cell transcriptomics (scRNA-Seq) explores cellular diversity at the gene expression level. Due to the inherent sparsity and noise in scRNA-Seq data and the uncertainty on the types of sequenced cells, effective clustering and cell type annotation are essential. The graph-based clustering of scRNA-Seq data is a simple yet powerful approach that presents data as a "shared nearest neighbour" graph and clusters the cells using graph clustering algorithms. These algorithms are dependent on several user-defined parameters. Here we present SUMA, a lightweight tool that uses a random forest model to predict the optimum number of neighbours to obtain the optimum clustering results. Moreover, we integrated our method with other commonly used methods in an RShiny application. SUMA can be used in a local environment (https://github.com/hkarakurt8742/SUMA) or as a browser tool (https://hkarakurt.shinyapps.io/suma/). Materials and methods: Publicly available scRNA-Seq datasets and 3 different graph-based clustering algorithms were used to develop SUMA, and a large range for number of neighbours and variant genes was taken into consideration. The quality of clustering was assessed using the adjusted Rand index (ARI) and true labels of each dataset. The data were split into training and test datasets, and the model was built and optimised using Scikit-learn (Python) and randomForest (R) libraries. Results: The accuracy of our machine learning model was 0.96, while the AUC of the ROC curve was 0.98. The model indicated that the number of cells in scRNA-Seq data is the most important feature when deciding the number of neighbours. Conclusion: We developed and evaluated the SUMA model and implemented the method in the SUMAShiny app, which integrates SUMA with different clustering methods and enables nonbioinformatician users to cluster and visualise their scRNA data easily. The SUMAShiny app is available both for desktop and browser use. [ABSTRACT FROM AUTHOR]

Spatial Autoregressive (SAR) models are used to model the relationship between variables within a specific region or location, considering the influence of neighboring variables, and have received considerable attention in recent years. However, when the impact of exogenous variables becomes notably pronounced, an alternative approach is warranted. Spatial Expansion, coupled with the Casetti model approach, serves as an extension of the SAR model, accommodating the influence of these exogenous variables. This modeling technique finds application in the realm of rainfall prediction, where exogenous factors, such as air temperature, humidity, solar irradiation, wind speed, and surface pressure, play pivotal roles. Consequently, this research aimed to combine the SAR and Spatial Expansion models through the Casetti model approach, leading to the creation of the Spatial Autoregressive Exogenous (SAR-X) model. The SAR-X was employed to forecast the rainfall patterns in the West Java region, utilizing data obtained from the National Aeronautics and Space Administration Prediction of Worldwide Energy Resources (NASA POWER) dataset. The practical execution of this research capitalized on the computational capabilities of the RStudio software version 2022.12.0. Within the framework of this investigation, a comprehensive and integrated RStudio script, seamlessly incorporated into the RShiny web application, was developed so that it is easy to use. [ABSTRACT FROM AUTHOR]

Spatial Autoregressive (SAR) models are used to model the relationship between variables within a specific region or location, considering the influence of neighboring variables, and have received considerable attention in recent years. However, when the impact of exogenous variables becomes notably pronounced, an alternative approach is warranted. Spatial Expansion, coupled with the Casetti model approach, serves as an extension of the SAR model, accommodating the influence of these exogenous variables. This modeling technique finds application in the realm of rainfall prediction, where exogenous factors, such as air temperature, humidity, solar irradiation, wind speed, and surface pressure, play pivotal roles. Consequently, this research aimed to combine the SAR and Spatial Expansion models through the Casetti model approach, leading to the creation of the Spatial Autoregressive Exogenous (SAR-X) model. The SAR-X was employed to forecast the rainfall patterns in the West Java region, utilizing data obtained from the National Aeronautics and Space Administration Prediction of Worldwide Energy Resources (NASA POWER) dataset. The practical execution of this research capitalized on the computational capabilities of the RStudio software version 2022.12.0. Within the framework of this investigation, a comprehensive and integrated RStudio script, seamlessly incorporated into the RShiny web application, was developed so that it is easy to use.

We present MultiEditR (Multiple Edit Deconvolution by Inference of Traces in R), the first algorithm specifically designed to detect and quantify RNA editing from Sanger sequencing (z.umn.edu/multieditr). Although RNA editing is routinely evaluated by measuring the heights of peaks from Sanger sequencing traces, the accuracy and precision of this approach has yet to be evaluated against gold standard next-generation sequencing methods. Through a comprehensive comparison to RNA sequencing (RNA-seq) and amplicon-based deep sequencing, we show that MultiEditR is accurate, precise, and reliable for detecting endogenous and programmable RNA editing.

Abstract Background Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. Still, such exploration is challenging as there is a need for visualizations that are tailored for the purpose. Results The OmicLoupe software was developed to facilitate visual data exploration and provides more than 15 interactive cross-dataset visualizations for omics data. It expands visualizations to multiple datasets for quality control, statistical comparisons and overlap and correlation analyses, while allowing for rapid inspection and downloading of selected features. The usage of OmicLoupe is demonstrated in three different studies, where it allowed for detection of both technical data limitations and biological trends across different omic layers. An example is an analysis of SARS-CoV-2 infection based on two previously published studies, where OmicLoupe facilitated the identification of gene products with consistent expression changes across datasets at both the transcript and protein levels. Conclusions OmicLoupe provides fast exploration of omics data with tailored visualizations for comparisons within and across data layers. The interactive visualizations are highly informative and are expected to be useful in various analyses of both newly generated and previously published data. OmicLoupe is available at quantitativeproteomics.org/omicloupe

Background: Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. Still, such exploration is challenging as there is a need for visualizations that are tailored for the purpose. Results: The OmicLoupe software was developed to facilitate visual data exploration and provides more than 15 interactive cross-dataset visualizations for omics data. It expands visualizations to multiple datasets for quality control, statistical comparisons and overlap and correlation analyses, while allowing for rapid inspection and downloading of selected features. The usage of OmicLoupe is demonstrated in three different studies, where it allowed for detection of both technical data limitations and biological trends across different omic layers. An example is an analysis of SARS-CoV-2 infection based on two previously published studies, where OmicLoupe facilitated the identification of gene products with consistent expression changes across datasets at both the transcript and protein levels. Conclusions: OmicLoupe provides fast exploration of omics data with tailored visualizations for comparisons within and across data layers. The interactive visualizations are highly informative and are expected to be useful in various analyses of both newly generated and previously published data. OmicLoupe is available at quantitativeproteomics.org/omicloupe [ABSTRACT FROM AUTHOR]

Abstract Background Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research. Results We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics. Conclusions WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.

To streamline the analysis and visualization of bacterial growth and gene expression data obtained by microtitre plate readers, we developed BactEXTRACT, an intuitive, easy-to-use R Shiny application. BactEXTRACT simplifies the transition from raw optical density, fluorescence and luminescence measurements to publication-ready plots. This package offers a user-friendly interface that reduces the complexity involved in growth curve and gene expression analysis and is generally applicable. BactEXTRACT is available at https://veeninglab.com/bactextract., Competing Interests: The authors declare that there are no conflicts of interest., (© 2024 The Authors.)

Background: Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research. Results: We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics. Conclusions: WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets. [ABSTRACT FROM AUTHOR]

This work reports the release and the usability of the dimensionality reduction app, an R application developed with the RShiny package to reduce data dimensionality using filters, resolution reduction, and algorithms based on parametric and non-parametric approaches. This application accepts data directly from.txt,.csv,.xlsx file extensions, and R data files directly exported by the data handling app presented in the Chemometrics web app's part 1: Data handling manuscript. The idea is to use the data directly from the instrument or preprocess it with the first app. Therefore, using the application does not require a deep knowledge of R software or matrix manipulation. The dimensionality reduction app allows performing basic Preprocessing such as mean centering and autoscaling, some adequacy testing, some filtering methods to reduce the data dimensionality, cluster analysis, diagnosis of the number of clusters, parametric and non-parametric based algorithms for dimensionality reduction and exploratory analysis, such as PCA and T-SNE respectively. Three datasets will be used for data dimensionality reduction and exploratory analysis. All the figures presented in this manuscript were directly exported from the dimensionality reduction app to highlight its functionalities. The main idea of this application is to allow chemometrics users to perform several strategies for dimensionality reduction and exploratory analysis even with no knowledge of programming language. Besides, the dimensionality reduction app is an open-access code available to be used on RStudio free environment at the software or cloud computing using computers, tablets, smartphones, or similar devices, even without installing anything for usage. • Open-source web app developed in R for dimensionality reduction and exploratory analysis. • Data adequacy test, variable preprocessing, filtering methods and simple resolution reduction. • Cluster Analysis and diagnosis tools to evaluate the number of clusters. • Parametric methods for dimensionality reduction and exploratory analysis. • Non-Parametric methods for dimensionality reduction and exploratory analysis. [ABSTRACT FROM AUTHOR]

This work reports the release and the usability of the data handling app, an R application, to perform an initial evaluation and treatment of the data. This application allows using the data directly from the analytical instrument, so it does not require a deep knowledge of R software for the user. The data handling app allows removing variables or samples, selecting a region or interesting variables, performing basic statistical analysis, descriptive analysis, several data imputations, spectra transformation, variables preprocessing, and normality-inducing transformation. Three datasets with some common features of chemical data were pretreated to highlight the app's usability. So, the main idea of this application is to allow chemometrics users to perform all the basic data pretreatment properly and perform an initial analysis of the data even with no knowledge of R programming. Besides, the data handling app is an open-access code available to be used on RStudio free environment at the computer or on cloud computing using computers, tablets, smartphones, or similar devices, even without installing any software. • Open-source web app developed in R software for chemometrics data pretreatment. • Descriptive analysis and evaluation of the normal distribution. • Missing data handling by exclude variables or input missing values. • Samples and variables pretreatment to solve several drawbacks present in chemical data. [ABSTRACT FROM AUTHOR]

We present MultiEditR (Multiple Edit Deconvolution by Inference of Traces in R), the first algorithm specifically designed to detect and quantify RNA editing from Sanger sequencing (z.umn.edu/multieditr). Although RNA editing is routinely evaluated by measuring the heights of peaks from Sanger sequencing traces, the accuracy and precision of this approach has yet to be evaluated against gold standard next-generation sequencing methods. Through a comprehensive comparison to RNA sequencing (RNA-seq) and amplicon-based deep sequencing, we show that MultiEditR is accurate, precise, and reliable for detecting endogenous and programmable RNA editing., Competing Interests: The authors declare no competing interests., (© 2021 The Authors.)

Health economic evaluation models have traditionally been built in Microsoft Excel, but more sophisticated tools are increasingly being used as model complexity and computational requirements increase. Of all the programming languages, R is most popular amongst health economists because it has a plethora of user created packages and is highly flexible. However, even with an integrated development environment such as R Studio, R lacks a simple point and click user interface and therefore requires some programming ability. This might make the switch from Microsoft Excel to R seem daunting, and it might make it difficult to directly communicate results with decisions makers and other stakeholders. The R package Shiny has the potential to resolve this limitation. It allows programmers to embed health economic models developed in R into interactive web browser based user interfaces. Users can specify their own assumptions about model parameters and run different scenario analyses, which, in the case of regular a Markov model, can be computed within seconds. This paper provides a tutorial on how to wrap a health economic model built in R into a Shiny application. We use a four-state Markov model developed by the Decision Analysis in R for Technologies in Health (DARTH) group as a case-study to demonstrate main principles and basic functionality. A more extensive tutorial, all code, and data are provided in a  GitHub repository., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Smith R and Schneider P.)